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Protein

Carbon monoxide dehydrogenase

Gene

cooS

Organism
Rhodospirillum rubrum
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Allows growth in a CO-dependent manner in the dark. CODH oxidizes carbon monoxide coupled, via CooF, to the reduction of a hydrogen cation by a hydrogenase (possibly CooH).By similarity

Catalytic activityi

CO + H2O + 2 oxidized ferredoxin = CO2 + 2 reduced ferredoxin + 2 H+.By similarity

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi41 – 411Iron-sulfur 1 (4Fe-4S); shared with dimeric partner1 Publication
Metal bindingi49 – 491Iron-sulfur 1 (4Fe-4S); shared with dimeric partner1 Publication
Metal bindingi50 – 501Iron-sulfur 2 (4Fe-4S)1 Publication
Metal bindingi53 – 531Iron-sulfur 2 (4Fe-4S)1 Publication
Metal bindingi58 – 581Iron-sulfur 2 (4Fe-4S)1 Publication
Metal bindingi72 – 721Iron-sulfur 2 (4Fe-4S)1 Publication
Metal bindingi265 – 2651Nickel-iron-sulfur (Ni-4Fe-4S); via tele nitrogen1 Publication
Metal bindingi300 – 3001Nickel-iron-sulfur (Ni-4Fe-4S)1 Publication
Metal bindingi338 – 3381Nickel-iron-sulfur (Ni-4Fe-4S)1 Publication
Metal bindingi451 – 4511Nickel-iron-sulfur (Ni-4Fe-4S)1 Publication
Metal bindingi481 – 4811Nickel-iron-sulfur (Ni-4Fe-4S)1 Publication
Metal bindingi531 – 5311Nickel-iron-sulfur (Ni-4Fe-4S)1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, Nickel

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16431.

Names & Taxonomyi

Protein namesi
Recommended name:
Carbon monoxide dehydrogenase (EC:1.2.7.4By similarity)
Short name:
CODH
Gene namesi
Name:cooS
OrganismiRhodospirillum rubrum
Taxonomic identifieri1085 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodospirillalesRhodospirillaceaeRhodospirillum

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Cytoplasm, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi265 – 2651H → V: Great decrease in activity; diminishes incorporation of nickel. Displays hydroxylamine reductase activity. 1 Publication
Mutagenesisi531 – 5311C → A: Displays hydrogenase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 639638Carbon monoxide dehydrogenasePRO_0000157139Add
BLAST

Expressioni

Inductioni

By carbon monoxide; under anaerobic conditions.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi269796.Rru_A1427.

Structurei

Secondary structure

1
639
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi30 – 378Combined sources
Helixi42 – 465Combined sources
Beta strandi62 – 665Combined sources
Helixi76 – 10934Combined sources
Turni110 – 1123Combined sources
Helixi122 – 13110Combined sources
Turni137 – 1393Combined sources
Helixi141 – 15414Combined sources
Turni155 – 1573Combined sources
Helixi166 – 1716Combined sources
Helixi174 – 18310Combined sources
Helixi190 – 20011Combined sources
Helixi209 – 23830Combined sources
Beta strandi244 – 2507Combined sources
Beta strandi257 – 2659Combined sources
Helixi267 – 27913Combined sources
Turni280 – 2823Combined sources
Helixi283 – 2864Combined sources
Beta strandi292 – 2987Combined sources
Helixi299 – 30810Combined sources
Beta strandi313 – 3153Combined sources
Turni318 – 3214Combined sources
Helixi322 – 3254Combined sources
Beta strandi331 – 3344Combined sources
Beta strandi336 – 3383Combined sources
Helixi343 – 3486Combined sources
Beta strandi353 – 3564Combined sources
Beta strandi366 – 3683Combined sources
Helixi373 – 3753Combined sources
Helixi376 – 39116Combined sources
Beta strandi406 – 4105Combined sources
Helixi414 – 4229Combined sources
Helixi430 – 43910Combined sources
Beta strandi440 – 4423Combined sources
Beta strandi444 – 4485Combined sources
Helixi460 – 47112Combined sources
Beta strandi474 – 4796Combined sources
Helixi480 – 48910Combined sources
Helixi494 – 5007Combined sources
Helixi503 – 51513Combined sources
Beta strandi518 – 5203Combined sources
Beta strandi524 – 5318Combined sources
Helixi534 – 54714Combined sources
Turni552 – 5543Combined sources
Beta strandi555 – 5617Combined sources
Helixi567 – 57913Combined sources
Beta strandi582 – 5876Combined sources
Turni590 – 5934Combined sources
Helixi595 – 6028Combined sources
Helixi604 – 6085Combined sources
Beta strandi612 – 6154Combined sources
Helixi619 – 63517Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JQKX-ray2.80A/B/C/D/E/F1-639[»]
DisProtiDP00239.
ProteinModelPortaliP31896.
SMRiP31896. Positions 28-637.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP31896.

Family & Domainsi

Domaini

Cluster B is an all-cysteinyl-liganded 4Fe-4S cluster; cluster C is a mixed Ni-Fe-S cluster which is the active site of CO oxidation. Cluster D is also an all-cysteinyl-liganded 4Fe-4S cluster that bridges the two subunits of the CODH dimer.By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CJG. Bacteria.
COG1151. LUCA.

Family and domain databases

Gene3Di1.20.1270.30. 1 hit.
3.40.50.2030. 2 hits.
InterProiIPR016101. CO_DH_a-bundle.
IPR010047. CODH.
IPR004137. HCP/CODH.
IPR011254. Prismane-like.
IPR016099. Prismane-like_a/b-sand.
[Graphical view]
PfamiPF03063. Prismane. 1 hit.
[Graphical view]
PIRSFiPIRSF005023. CODH. 1 hit.
SUPFAMiSSF56821. SSF56821. 1 hit.
TIGRFAMsiTIGR01702. CO_DH_cata. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P31896-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTHHDCAHCS SDACATEMLN LAEANSIETA WHRYEKQQPQ CGFGSAGLCC
60 70 80 90 100
RICLKGPCRI DPFGEGPKYG VCGADRDTIV ARHLVRMIAA GTAAHSEHGR
110 120 130 140 150
HIALAMQHIS QGELHDYSIR DEAKLYAIAK TLGVATEGRG LLAIVGDLAA
160 170 180 190 200
ITLGDFQNQD YDKPCAWLAA SLTPRRVKRL GDLGLLPHNI DASVAQTMSR
210 220 230 240 250
THVGCDADPT NLILGGLRVA MADLDGSMLA TELSDALFGT PQPVVSAANL
260 270 280 290 300
GVMKRGAVNI AVNGHNPMLS DIICDVAADL RDEAIAAGAA EGINIIGICC
310 320 330 340 350
TGHEVMMRHG VPLATNYLSQ ELPILTGALE AMVVDVQCIM PSLPRIAECF
360 370 380 390 400
HTQIITTDKH NKISGATHVP FDEHKAVETA KTIIRMAIAA FGRRDPNRVA
410 420 430 440 450
IPAFKQKSIV GFSAEAVVAA LAKVNADDPL KPLVDNVVNG NIQGIVLFVG
460 470 480 490 500
CNTTKVQQDS AYVDLAKSLA KRNVLVLATG CAAGAFAKAG LMTSEATTQY
510 520 530 540 550
AGEGLKGVLS AIGTAAGLGG PLPLVMHMGS CVDNSRAVAL ATALANKLGV
560 570 580 590 600
DLSDLPLVAS APECMSEKAL AIGSWAVTIG LPTHVGSVPP VIGSQIVTKL
610 620 630
VTETAKDLVG GYFIVDTDPK SAGDKLYAAI QERRAGLGL
Length:639
Mass (Da):66,854
Last modified:July 1, 1993 - v1
Checksum:iDCADD7C13D8D85B8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U65510 Genomic DNA. Translation: AAC45123.1.
PIRiC42957.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U65510 Genomic DNA. Translation: AAC45123.1.
PIRiC42957.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JQKX-ray2.80A/B/C/D/E/F1-639[»]
DisProtiDP00239.
ProteinModelPortaliP31896.
SMRiP31896. Positions 28-637.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi269796.Rru_A1427.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105CJG. Bacteria.
COG1151. LUCA.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16431.

Miscellaneous databases

EvolutionaryTraceiP31896.

Family and domain databases

Gene3Di1.20.1270.30. 1 hit.
3.40.50.2030. 2 hits.
InterProiIPR016101. CO_DH_a-bundle.
IPR010047. CODH.
IPR004137. HCP/CODH.
IPR011254. Prismane-like.
IPR016099. Prismane-like_a/b-sand.
[Graphical view]
PfamiPF03063. Prismane. 1 hit.
[Graphical view]
PIRSFiPIRSF005023. CODH. 1 hit.
SUPFAMiSSF56821. SSF56821. 1 hit.
TIGRFAMsiTIGR01702. CO_DH_cata. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Genetic and physiological characterization of the Rhodospirillum rubrum carbon monoxide dehydrogenase system."
    Kerby R.L., Hong S.S., Ensign S.A., Coppoc L.J., Ludden P.W., Roberts G.P.
    J. Bacteriol. 174:5284-5294(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-26.
    Strain: UR1.
  2. "Characterization of the CO-induced, CO-tolerant hydrogenase from Rhodospirillum rubrum and the gene encoding the large subunit of the enzyme."
    Fox J.D., Kerby R.L., Roberts G.P., Ludden P.W.
    J. Bacteriol. 178:1515-1524(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: UR1.
  3. "Substitution of valine for histidine 265 in carbon monoxide dehydrogenase from Rhodospirillum rubrum affects activity and spectroscopic states."
    Spangler N.J., Meyers M.R., Gierke K.L., Kerby R.L., Roberts G.P., Ludden P.W.
    J. Biol. Chem. 273:4059-4064(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF HIS-265.
  4. "Converting the NiFeS carbon monoxide dehydrogenase to a hydrogenase and a hydroxylamine reductase."
    Heo J., Wolfe M.T., Staples C.R., Ludden P.W.
    J. Bacteriol. 184:5894-5897(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF CYS-531.
  5. Cited for: REVIEW.
  6. "Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase."
    Drennan C.L., Heo J., Sintchak M.D., Schreiter E., Ludden P.W.
    Proc. Natl. Acad. Sci. U.S.A. 98:11973-11978(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH NICKEL-IRON-SULFUR CLUSTER (NI-4FE-4S) AND IRON-SULFUR (4FE-4S), COFACTOR, SUBUNIT.

Entry informationi

Entry nameiCOOS_RHORU
AccessioniPrimary (citable) accession number: P31896
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: July 6, 2016
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Methyl viologen can act as acceptor. Inactivated by O2.

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.